## Breaking Changes Major reorganisation of the codebase to support packaging with setuptools. Move all Python modules under the diphtoscan package. Relocate data files inside the diphtoscan package. Update all imports to use relative imports. Add pyproject.toml to enable package building and installation. ## Added Support for building and installing the project as a Python package using setuptools. Add JolyTree as a dependency in environment.yml. Include package data during installation to ensure correct runtime behavior. Add a local fallback database for toxigenic profiles published before 01/01/2025. ## Changed Update JolyTree execution to avoid shell calls and modernize dependency resolution. Adapt code to support different key names between AMRFinderPlus version 3 and 4. Automatically fall back to the local toxigenic profiles database when BIGSdb returns no result.